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Although historical records of introductions that trigger successful biological invasions are common, subsequent patterns of dispersal and colonisation routes are unclear. We use microsatellites to examine genetic population structuring of established invasive brown trout (Salmo trutta) populations in Newfoundland, Canada, for evidence of “natural” dispersal, human-mediated introductions, and colonisation routes. We also explored ancestry of contemporary populations relative to presumed progenitors. Results analysed using STRUCTURE, DAPC, a NJ tree and FST comparisons support records of historical introductions; current Newfoundland populations are largely descended from Scottish stock, with St. John’s the primary introduction site. Subsequent dispersal of these trout was facilitated principally by anadromy, largely consistent with a classic stepping-stone model, with significant isolation-by-distance. With one exception, dispersal along the north and south coasts of the Avalon peninsula appears to be natural and independent, involving stochastic processes resulting in unique outcomes for population composition. This study is a good example of dispersal patterns during a contemporary invasion underscoring the potential for non-anadromous founders to re-express anadromy, facilitating colonization of distant sites.

Many post-smolt tissues were collected and screened as part of the EU funded SALSEA-Merge (Project No. 212529) part of the Seventh Framework Programme and co-sponsored by the Atlantic Salmon Trust and the Total Foundation., Gilbey, J., Utne, K.R., Wennevik, V., Beck, A.C., Kausrud, K., Hindar, K., Garcia de Leaniz, C., Cherbonnel, C., Coughlan, J., Cross, T.F., Dillane, E., Ensing, D., García-Vázquez, E., Hole, L.R., Holm, M., Holst, J.C., Jacobsen, J.A., Jensen, A.J., Karlsson, S., Ó Maoiléidigh, N., Mork, K.A., Nielsen, E.E., Nøttestad, L., Primmer, C.R., Prodöhl, P., Prusov, S., Stevens, J.R., Thomas, K., Whelan, K., McGinnity, P., Verspoor, E.

Funding: This work was supported by the National Geographic Society [grant number EC-53116R-18]. Sexual segregation is common among marine mammals, leading to intraspecific differences in diet, diving behaviour, home range size and even latitudinal distribution and migratory patterns. Sperm whales Physeter macrocephalus present one of the most extreme examples of sexual dimorphism both in size and social structure, with males and females segregating at different latitudes across most of their range, but the underlying ecological drivers remain unclear. Studying fine-scale dietary and habitat differences where the sexes occur in sympatry could therefore provide insights into the mechanisms underpinning their large-scale segregation. In this study, we analysed the carbon and nitrogen stable isotope values in the skin of males and females from an isolated, endangered population inhabiting the Mediterranean Sea, sampled in a region where the sexes occur and feed regularly in the summer months but show subtle differences in habitat preference. We found marked differences in both carbon and nitrogen isotopic values between the sexes, indicating that they could be targeting prey items in different trophic levels and habitats. Combined with the evidence from habitat modelling studies, our results suggest that female and male sperm whales segregate even in the latitudinally restricted Mediterranean population, at a much smaller scale. This sympatric, fine-scale sexual segregation suggests that reduction of competition may have been a key factor in the evolution of the social structure and large-scale latitudinal segregation of this species. Postprint

Territorial animals often respond less aggressively to neighbours than strangers. This ‘dear enemy’ effect is hypothesized to be adaptive by reducing unnecessary aggressive interactions with non-threatening individuals. A key prediction of this hypothesis, that individual fitness will be affected by variation in the speed and the extent to which individuals reduce their aggression towards neighbours relative to strangers, has never been tested. We used a series of song playbacks to measure the change in response of male great tits to a simulated establishment of a neighbour on an adjacent territory during early stages of breeding, as an assay of individuals’ tendencies to form dear enemy relationships. Males reduced their approach to the speaker and sang fewer songs on later playback repetitions. However, only some males exhibited dear enemy behaviour by responding more strongly to a subsequent stranger playback, and when the playback procedure was repeated on a subset of males, there was some indication for consistent differences among individuals in the expression of dear enemy behaviour. We monitored nests and analysed offspring paternity to determine male reproductive success. Individuals that exhibited dear enemy behaviour towards the simulated neighbour did not suffer any costs associated with loss of paternity, but there was also no evidence of reproductive benefits, and no net effect on reproductive fitness. The general ability to discriminate between neighbours and strangers is likely adaptive, but benefits are probably difficult to detect because of the indirect link between individual variation in dear enemy behaviour and reproductive fitness and because of the complex range of mechanisms affecting relations with territorial neighbours. Significance statement: The dear enemy effect, in which animals respond less aggressively to familiar neighbours compared to strangers, is probably beneficial because it reduces aggressive interactions with non-threatening individuals. However, no study has ever tested whether there actually are fitness benefits for individuals with a greater tendency to form dear enemy relationships. Our study used experimental playbacks to simulate neighbours and strangers, and we found no relationship between dear enemy behaviour and reproductive success in a songbird. However, our approach to test adaptive hypotheses of this widespread territorial behaviour and our longitudinal playback design to examine the development of familiarity towards a neighbour and discrimination of neighbours and strangers are likely to be important tools to advance our understanding of territorial behaviour and individual recognition.

The occurrence of alternative morphs within populations is common but the underlying molecular mechanisms remain poorly understood. Many animals, for example, exhibit facultative migration, where two or more alternative migratory tactics (AMTs) coexist within populations. In certain salmonid species, some individuals remain in natal rivers all their lives, whilst others (in particular, females) migrate to sea for a period of marine growth. Here we performed transcriptional profiling (“RNA-seq”) of the brain and liver of male and female brown trout to understand the genes and processes that differentiate migratory and residency morphs (AMT-associated genes) and how they may differ in expression between the sexes. We found tissue-specific differences with greater number of genes expressed differentially in the liver (n = 867 genes) compared to the brain (n = 10) between the morphs. Genes with increased expression in resident livers were enriched for Gene Ontology terms associated with metabolic processes, highlighting key molecular-genetic pathways underlying the energetic requirements associated with divergent migratory tactics. In contrast, smolt-biased genes were enriched for biological processes such as response to cytokines, suggestive of possible immune function differences between smolts and residents. Finally, we identified evidence of sex-biased gene expression for AMT-associated genes in the liver (n = 18) but not the brain. Collectively, our results provide insights into tissue-specific gene expression underlying the production of alternative life-histories within and between the sexes, and point towards a key role for metabolic processes in the liver in mediating divergent physiological trajectories of migrants versus residents.

The interaction of an array of volatile organic compounds (VOCs) termed bacterial volatile compounds (BVCs) with plants is now a major area of study under the umbrella of plant-microbe interactions. Many growth systems have been developed to determine the nature of these interactions in vitro. However, each of these systems have their benefits and drawbacks with respect to one another and can greatly influence the end-point interpretation of the BVC effect on plant physiology. To address the need for novel growth systems in BVC-plant interactions, our study investigated the use of a passively ventilated growth system, made possible via Microbox® growth chambers, to determine the effect of BVCs emitted by six bacterial isolates from the genera Bacillus, Serratia, and Pseudomonas. Solid-phase microextraction GC/MS was utilized to determine the BVC profile of each bacterial isolate when cultured in three different growth media each with varying carbon content. 66 BVCs were identified in total, with alcohols and alkanes being the most abundant. When cultured in tryptic soy broth, all six isolates were capable of producing 2,5-dimethylpyrazine, however BVC emission associated with this media were deemed to have negative effects on plant growth. The two remaining media types, namely Methyl Red-Voges Proskeur (MR-VP) and Murashige and Skoog (M + S), were selected for bacterial growth in co-cultivation experiments with Solanum tuberosum L. cv. ‘Golden Wonder.’ The BVC emissions of Bacillus and Serratia isolates cultured on MR-VP induced alterations in the transcriptional landscape of potato across all treatments with 956 significantly differentially expressed genes. This study has yielded interesting results which indicate that BVCs may not always broadly upregulate expression of defense genes and this may be due to choice of plant-bacteria co-cultivation apparatus, bacterial growth media and/or strain, or likely, a complex interaction between these factors. The multifactorial complexities of observed effects of BVCs on target organisms, while intensely studied in recent years, need to be further elucidated before the translation of lab to open-field applications can be fully realized.

Cryptic species pose a particular challenge to biologists in the context of life history investigations because of the difficulty in their field discrimination. Additionally, there is normally a lag in their widespread acceptance by the scientific community once they are formally recognised. These two factors might constrain our ability to properly assess the conservation status of the different species conforming a cryptic complex. In this study, we analysed isotopic and genetic data to shed light into the still unclear wintering grounds, population size and evolutionary history of the Iberian chiffchaff (Phylloscopus ibericus), a species included within the Common chiffchaff (Phylloscopus collybita) until two decades ago due to their phenotypic similarity. We used molecular methods to identify spring‐migrating Phylloscopus species captured in northern Iberia, and by comparing the Hydrogen isotopic ratios of their claw tips (δ2Hc; which would reflect the signatures of their wintering grounds), we detected that δ2Hc values of Iberian chiffchaffs were similar to Willow warblers (Phylloscopus trochilus; a renowned trans‐Saharan migrant), and higher than Common chiffchaffs (mostly a pre‐Saharan migrant). These results strongly support the idea that Iberian chiffchaffs winter in tropical Africa. We additionally reconstructed the phylogeny and evolutionary history of the Iberian chiffchaff's clade using mitochondrial and nuclear markers. Our results revealed relatively high values of nucleotide diversity (and, hence, high Ne) for the species that were greater than the values of the Common/Iberian most recent common ancestor. This suggests that the Iberian chiffchaff did not experience strong bottlenecks after diverging from the Common chiffchaff approximately one million years ago. Ultimately, our study provides another illustrative example of how isotopic and genetic analysis tools can help to enhance our understanding of avian ecology and evolution.

M.N. was funded by a Crawford‐Hayes studentship and National Parks and Wildlife Service (NPWS), Department of Culture, Heritage and Gaeltacht, Ireland. E.D. was supported by the Beaufort Marine Research Award in Fish Population Genetics funded by the Irish Government under the Sea Change Programme. Financial support for A.D.F. was provided by the Welsh Government and Higher Education Funding Council for Wales through the Sêr Cymru National Research Network for Low Carbon, Energy and Environment, and from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska‐Curie grant agreement No. 663830. The functioning of marine protected areas (MPAs) designated for marine megafauna has been criticized due to the high mobility and dispersal potential of these taxa. However, dispersal within a network of small MPAs can be beneficial as connectivity can result in increased effective population size, maintain genetic diversity, and increase robustness to ecological and environmental changes making populations less susceptible to stochastic genetic and demographic effects (i.e., Allee effect). Here, we use both genetic and photo-identification methods to quantify gene flow and demographic dispersal between MPAs of a highly mobile marine mammal, the bottlenose dolphin Tursiops truncatus. We identify three populations in the waters of western Ireland, two of which have largely nonoverlapping core coastal home ranges and are each strongly spatially associated with specific MPAs. We find high site fidelity of individuals within each of these two coastal populations to their respective MPA. We also find low levels of demographic dispersal between the populations, but it remains unclear whether any new gametes are exchanged between populations through these migrants (genetic dispersal). The population sampled in the Shannon Estuary has a low estimated effective population size and appears to be genetically isolated. The second coastal population, sampled outside of the Shannon, may be demographically and genetically connected to other coastal subpopulations around the coastal waters of the UK. We therefore recommend that the methods applied here should be used on a broader geographically sampled dataset to better assess this connectivity. Publisher PDF

Atlantic salmon (Salmo salar L.) populations from different river origins mix in the North Atlantic during the marine life stage. To facilitate marine stock identification, we developed a genetic baseline covering the European component of the species’ range excluding the Baltic Sea, from the Russian River Megra in the north-east, the Icelandic Ellidaar in the west, and the Spanish Ulla in the south, spanning 3737 km North to South and 2717 km East to West. The baseline encompasses data for 14 microsatellites for 26 822 individual fish from 13 countries, 282 rivers, and 467 sampling sites. A hierarchy of regional genetic assignment units was defined using a combination of distance-based and Bayesian clustering. At the top level, three assignment units were identified comprising northern, southern, and Icelandic regions. A second assignment level was also defined, comprising eighteen and twenty-nine regional units for accurate individual assignment and mixed stock estimates respectively. The baseline provides the most comprehensive geographical coverage for an Atlantic salmon genetic data-set, and a unique resource for the conservation and management of the species in Europe. It is freely available to researchers to facilitate identification of the natal origin of European salmon.

Funding: Fyssen post-doctoral fellowship, Fondation Total, a bridge funding from the School of Biology of the University of St Andrews and People’s Trust for Endangered Species (ML). 1. Protecting species often involves the designation of protected areas, wherein suitable management strategies are applied either at the taxon or ecosystem level. Special Areas of Conservation (SACs) have been created in European waters under the Habitats Directive to protect bottlenose dolphins, Tursiops truncatus, which forms two ecotypes, pelagic and coastal. 2. The SACs have been designated in coastal waters based on photo‐identification studies that have indicated that bottlenose dolphins have relatively high site fidelity. However, individuals can carry out long‐distance movements, which suggests potential for demographic connectivity between the SACs as well as with other areas. 3. Connectivity can be studied using genetic markers. Previous studies on the species in this area used different sets of genetic markers and therefore inference on the fine‐scale population structure and demographic connectivity has not yet been made at a large scale. A common set of microsatellite markers was used in this study to provide the first comprehensive estimate of genetic structure of bottlenose dolphins in European Atlantic waters. 4. As in previous studies, a high level of genetic differentiation was found between coastal and pelagic populations. Genetic structure was defined at an unprecedented fine‐scale level for coastal dolphins, leading to identification of five distinct coastal populations inhabiting the following areas: Shannon estuary, west coast of Ireland, English Channel, coastal Galicia, east coast of Scotland and Wales/west Scotland. Demographic connectivity was very low among most populations with

The high level of exploitation and slow population growth rates of many elasmobranch species are causing worldwide concern about their status. Genetic methods offer the potential to gather information on the stock structure and conservation status of species with implications in the delineation of appropriate management units. However, despite several calls from the scientific community, they are still largely ignored in fisheries management. Here, we use genetic approaches to assess the population structure of the cuckoo ray (Leucoraja naevus), a species of skate that was recently designated as vulnerable in Irish waters by the International Union for Conservation of Nature. By genotyping individuals (n = 188) originating from a vast geographic area with nine microsatellite markers, we do not find evidence of population structuring but cuckoo rays in Irish waters seem to belong to a single genetically diverse panmictic population despite the restricted movements observed in closely related species. Cuckoo rays should therefore continue to be monitored as a single stock in this area.

While environmental DNA (eDNA) is becoming increasingly established in biodiversity monitoring of freshwater ecosystems, the use of eDNA surveys in the marine environment is still in its infancy. Here, we use two approaches: targeted quantitative PCR (qPCR) and whole-genome enrichment capture followed by shotgun sequencing in an effort to amplify killer whale DNA from seawater samples. Samples were collected in close proximity to killer whales in inshore and offshore waters, in varying sea conditions and from the surface and subsurface but none returned strongly positive detections of killer whale eDNA. We validated our laboratory methodologies by successfully amplifying a dilution series of a positive control of killer whale DNA. Furthermore, DNA of Atlantic mackerel, which was present at all sites during sampling, was successfully amplified from the same seawater samples, with positive detections found in ten of the eighteen eDNA extracts. We discuss the various eDNA collection and amplification methodologies used and the abiotic and biotic factors that influence eDNA detection. We discuss possible explanations for the lack of positive killer whale detections, potential pitfalls, and the apparent limitations of eDNA for genetic research on cetaceans, particularly in offshore regions.

Fishery managers need robust ways of objectively estimating the quantitative composition of fish stocks, by species and age-class, from representative samples of populations. Dual-frequency identification sonar data were used to first visually identify fish to a broad taxon (Salmonidae). Subsequently, kernel-density estimations, based on calibrated size-at-age data for the possible component species, were used to assign sonar observations both to species (Atlantic Salmon Salmo salar or Brown Trout Salmo trutta) and age-classes within species. The calculations are illustrated for alternative sets of calibration data. To obtain close and relevant fits, the approach fundamentally relies on having accurate and fully representative subcomponent distributions. Firmer inferences can be made if the component data sets correspond closely to the target information in both time and space. Given carefully chosen suites of component data, robust population composition estimates with narrow confidence intervals...

Globally, collisions between wildlife and aircraft are a serious threat to aviation safety. While reported collisions have increased in recent years, the impact of these collisions on air safety is rarely quantified. Here, we report all bat collisions (bat strikes) with civil aircraft known to have occurred in the Republic of Ireland over the 10-year interval, 2006–2015. Morphological and/or DNA identification techniques were used to identify chiropteran specimens to species level. In total, carcasses or remains from five bat strikes—three Leisler’s Nyctalus leisleri, one Soprano Pipistrelle Pipistrellus pygmaeus, and one Natterer’s Myotis nattereri—were recovered. The collisions are discussed in the context of (a) the rate of chiropteran strikes in relation to the number of civil aircraft movements and (b) possible damage caused to aircraft. Overall, however, bat strikes with aircraft appear to have a negligible effect on civil aircraft safety.

By combining next-generation sequencing technology (454) and reduced representation library (RRL) construction, the rapid and economical isolation of over 25 000 potential single-nucleotide polymorphisms (SNP) and >6000 putative microsatellite loci from c. 2% of the genome of the non-model teleost, Atlantic cod Gadus morhua from the Celtic Sea, south of Ireland, was demonstrated. A small-scale validation of markers indicated that 80% (11 of 14) of SNP loci and 40% (6 of 15) of the microsatellite loci could be amplified and showed variability. The results clearly show that small-scale next-generation sequencing of RRL genomes is an economical and rapid approach for simultaneous SNP and microsatellite discovery that is applicable to any species. The low cost and relatively small investment in time allows for positive exploitation of ascertainment bias to design markers applicable to specific populations and study questions.

The present study examined the contemporary genetic composition of the Eurasian badger, Meles meles, in Ireland, Britain and Western Europe, using six nuclear microsatellite loci and a 215-bp fragment of the mitochondrial DNA control region. Significant population structure was evident within Europe (global multilocus microsatellite FST = 0.205, P < 0.001; global mitochondrial control region ΦST = 0.399, P < 0.001). Microsatellite-based cluster analyses detected one population in Ireland, whereas badgers from Britain could be subdivided into several populations. Excluding the island populations of Ireland and Britain, badgers from Western Europe showed further structuring, with evidence of discrete Scandinavian, Central European, and Spanish populations. Mitochondrial DNA cluster analysis grouped the Irish population with Scandinavia and Spain, whereas the majority of British haplotypes grouped with those from Central Europe. The findings of the present study suggest that British and Irish badger populations colonized from different refugial areas, or that there were different waves of colonization from the source population. There are indications for the presence of an Atlantic fringe element, which has been seen in other Irish species. We discuss the results in light of the controversy about natural versus human-mediated introductions

The identification of localized discrete populations is particularly important to the management and conservation of animal species, especially in the marine environment, where potential for dispersal is high but barriers to gene flow are often not clear. We investigated population genetic structuring of bottlenose dolphins Tursiops truncatus found along the west coast of Ireland, with particular attention to the Shannon Estuary, which is the only candidate Special Area of Conservation designated for this species in Irish waters. A genetic structure analysis using 62 biopsy samples from free ranging dolphins and 23 necropsies from stranded dolphins revealed fine-scale population structure among three distinct populations. The Shannon Estuary population appears to be genetically isolated from adjacent coastal areas, with the exception of four animals sampled from a small group of six dolphins that are now resident in Cork Harbour (south coast) indicating ongoing gene flow or recent dispersal between these two areas. A second genetically distinct aggregation was identified in the Connemara–Mayo region, where recent photo-identification studies have suggested that dolphins found in this area show a degree of site fidelity. We found moderate nuclear (15 microsatellites) and low mitochondrial (544 bp of the control region) gene diversity in dolphins using the Shannon Estuary and the Connemara–Mayo region, while dolphins that stranded along the coast showed markedly higher levels of gene diversity at both classes of markers. Specifically, these stranded dolphins formed a third genetically distinct cluster, which may be part of a larger pelagic population, as also suggested by the high levels of gene diversity. These results provide new insights into population structure of bottlenose dolphins in Irish waters and will aid future management and conservation of the species in the eastern North Atlantic.

The analysis of stranding events and the application of molecular markers can be powerful tools to study cryptic biological aspects of delphinid species that occur mainly in open ocean habitat. In the present study, we investigated nuclear and mitochondrial genetic variability of Atlantic white-sided dolphins that stranded from 1990 to 2006 (n = 42) along the west coast of Ireland, using 8 microsatellite loci and 599 bp of the mitochondrial DNA control region. Results from both classes of markers are concordant with the hypothesis of a large random-mating population of white-sided dolphins along the west coast of Ireland. In addition, the analyses of 2 live mass stranding events (19 and 5 individuals, respectively) revealed that dolphins within each group were mainly unrelated to each other, suggesting dispersal of both sexes from the natal group (i.e., no natal phylopatry). Parentage analyses allowed the identification of mother-offspring pairs but ruled out all adult males as possible fathers. In combination with data on age of individuals, these results confirmed previous knowledge on life-history parameters, with sexually mature females ranging between 11 and 15 years of age and an interbirth interval of at least 2 years. The present study provides novel information on population and group composition of Atlantic white-sided dolphins along the west coast of Ireland, where population and social structure of the species are still poorly understood.

Microsatellite DNA loci, when used in population genetic studies, are usually assumed to be neutral (unaffected by natural selection, either directly or as a result of tight linkage), but this assumption is rarely tested. Here, the assumption of neutrality is examined using established methods, principally that based on the expected relationship between F ST and heterozygosity, at 12 putative neutral microsatellite loci utilised in a study of Atlantic herring Clupea harengus in the north east Atlantic (west of Great Britain and around Ireland) and in the Baltic Sea. All but two of these loci demonstrate relationships that suggest that they may be regarded as neutral genetic markers. Of the other two loci, however, one shows a relationship suggestive of the action of directional selection and the other of balancing natural selection, though other locus-specific effects may operate. Thus, the latter two loci may provide inaccurate inference if used in phylogeographic studies and also demonstrate the danger of assuming neutrality at all microsatellite loci without explicit testing. However, such loci, particularly those affected by directional as opposed to balancing selection, may be of great use in stock discrimination studies, and selected loci in general, have considerably potential in studies of adaptation.

Previous genetic studies using neutral markers such as allozymes, mtDNA and minisatellite loci have demonstrated varying amounts of population structure in cod Gadus morhua throughout the Atlantic. Microsatellite loci, which are potentially the most informative of presently available neutral genetic markers, have been applied extensively within western and eastern Atlantic areas but not on a range-wide basis. In the present study, six microsatellite DNA loci were used to screen cod samples from nine locations throughout the geographic range from the Scotian Shelf in the West Atlantic to the Barents and Baltic Seas in the east. Overall FST value was 0·03 (P= < 0·001) across all samples. Statistically significant population differences over all loci combined were evident between more geographically distant samples, using either heterogeneity tests or FST analysis, with at least one locus showing significant differences between all samples (prior to Bonferroni correction). A significant correlation was observed between genetic and geographical distance, suggesting a higher level of historical and contemporary gene flow between adjacent populations than more distant populations. Samples from either end of the geographic range (Scotian Shelf and Baltic Sea) were particularly distinct when analysed using the STRUCTURE programme and also showed a high level of self-assignment when individuals of either the Scotian Shelf or Baltic Sea were tested against the entire data set. The present microsatellite study demonstrates a high level of geographic population structure between the western Atlantic, middle and eastern Atlantic and Baltic Sea, and thus, the findings should be useful in devising overall management and conservation strategies for the species.

Two sequential year classes of Atlantic salmon parr, Salmo salar L., from 13 rivers throughout Ireland, genotyped at four widely used microsatellite loci, displayed comparable levels of intra-sample genetic variability to elsewhere in the species range. Temporal allele frequency differences were observed in only one riverine sample, whereas significant spatial differences were evident in all cases, with an overall FST value of 0.03. These spatial differences imply a high degree of natal homing. Two tributaries of a single major river system displayed variability comparable with that within the entire study, suggesting that large rivers may contain several separate tributary populations. Isolation-by-distance analysis suggests the presence of regional structure, which may have been obscured by inclusion of samples from some smaller rivers in Donegal Bay in the north west that are probably affected by incursions of cultured salmon from a nearby ranching operation. Although limited by the small number of loci screened, individual assignment analysis gave levels of self-assignment which would suggest that mixed stock analysis would be feasible as a management tool in Irish salmon fisheries, given the inclusion of larger numbers of microsatellite loci and more extensive coverage of salmon producing rivers.

Several studies have documented the genetic effects of intraspecific hybridization of cultured and wild Atlantic salmon (Salmo salar L.). However, the effect of salmon aquaculture on wild congeners is not so well understood. Diseases, introduced or increased in incidence by salmon aquaculture activities, may have an impact on co-occurring wild sea trout (Salmo trutta L.), as implied by the steep decline in sea trout numbers in many Irish, Scottish, and Norwegian rivers since the late 1980s, which may be linked to sea lice infestations associated with marine salmonid farming. Our data suggest that salmon farming and ocean ranching can indirectly affect, most likely mediated by disease, the genetics of cohabiting sea trout by reducing variability at major histocompatibility class I genes. We studied samples of DNA extracted from scales of sea trout in the Burrishoole River, in the west of Ireland, before and at intervals during aquaculture activities. In these samples, allelic variation at a microsatellite marker, tightly linked to a locus critical to immune response (Satr-UBA), was compared with variation at six neutral microsatellite loci. A significant decline in allelic richness and gene diversity at the Satr-UBA marker locus, observed since aquaculture started and which may indicate a selective response, was not reflected by similar reductions at neutral loci. Subsequent recovery of variability at the Satr-UBA marker, seen among later samples, may reflect an increased contribution by resident brown trout to the remaining sea trout stock.

Samples of Todaropsis eblanae from throughout the species range in east Atlantic and Mediterranean waters were screened for genetic variability at 1 minisatellite and 4 microsatellite loci. Extremely high levels of variability were observed within samples at all loci, with the mean observed heterozygosity per locus ranging from 0.82 to 0.91. Tests of allele frequency heterogeneity and measures of F ST (Wright's fixation index) suggest that significant genetic differentiation occurs between samples taken in African waters and those taken in European waters (overall F ST = 0.014, p < 0.001). Furthermore, significant differentiation was evident between the samples taken from South African waters and those taken from off Mauritania (between sample F ST = 0.012, p < 0.001). More subtle structuring was suggested within the European samples, largely attributable to differences between the Mediterranean sample and Atlantic samples (within Europe F ST = 0.002, p < 0.03). However, the high levels of heterozygosity associated with the examined loci means that biological implications of marginally significant statistical results must be considered. One consistent aspect of the observed variation is that the Mauritanian sample is more genetically differentiated from European samples than from the more geographically isolated South African sample. Homoplasy and historical events such as climatic cycles and post-glacial recolonisation are considered as possible explanations for the observed patterns of variation. In terms of stock structure, the findings suggest the presence of at least 3 genetically isolated populations in the east Atlantic, which has important implications for management and sustainability of this resource.

Understanding the extent, scale and genetic basis of local adaptation (LA) is important for conservation and management. Its relevance in salmonids at microgeographic scales, where dispersal (and hence potential gene flow) can be substantial, has however been questioned. Here, we compare the fitness of communally reared offspring of local and foreign Atlantic salmon Salmo salar from adjacent Irish rivers and reciprocal F1 hybrid crosses between them, in the wild ‘home’ environment of the local population. Experimental groups did not differ in wild smolt output but a catastrophic flood event may have limited our ability to detect freshwater performance differences, which were evident in a previous study. Foreign parr exhibited higher, and hybrids intermediate, emigration rates from the natal stream relative to local parr, consistent with genetically based behavioural differences. Adult return rates were lower for the foreign compared to the local group. Overall lifetime success of foreigners and hybrids relative to locals was estimated at 31% and 40% (mean of both hybrid groups), respectively. The results imply a genetic basis to fitness differences among populations separated by only 50 km, driven largely by variation in smolt to adult return rates. Hence even if supplementary stocking programs obtain broodstock from neighbouring rivers, the risk of extrinsic outbreeding depression may be high.

Seven tetranucleotide and three dinucleotide microsatellite loci were isolated from the short-beaked common dolphin (Delphinus delphis). Number of alleles and observed heterozygosity ranged from three to twelve (mean 8.4) and from 0.087 to 0.978 (mean 0.741), respectively. All loci were tested in four other odontocete species and showed polymorphisms in most locus–species combinations. This panel of nuclear markers will be useful for the investigation of population ecology and social interactions in common dolphins and other cetacean species.

Major histocompatibility complex (MHC) class I-linked microsatellite data and parental assignment data for a group of wild brown trout (Salmo trutta L.) provide evidence of closer spatial aggregation among fry sharing greater numbers of MHC class I alleles under natural conditions. This result confirms predictions from laboratory experiments demonstrating a hierarchical preference for association of fry sharing MHC alleles. Full-siblings emerge from the same nest (redd), and a passive kin association pattern arising from limited dispersal from the nest (redd effect) would predict that all such pairs would have a similar distribution. However, this study demonstrates a strong, significant trend for reduced distance between pairs of full-sibling fry sharing more MHC class I alleles reflecting their closer aggregation (no alleles shared, 311.5±(s.e.)21.03m; one allele shared, 222.2±14.49m; two alleles shared, 124.9±23.88m; P, HEA PRTLI Cycle 3; Beaufort Marine Research Award: Fish population genetics. Irish Government NDP (2007–2014) administered by the Marine Institute; Inland Fisheries Ireland; Science Foundation Ireland (Microbial Phylogeography 05/FE1/B882)

This work forms part of the SALSEA-Merge research project (Project No. 212529) and was funded by the European Union under theme six of the 7th Framework programme, Ellis, J.S., Gilbey, J., Armstrong, A., Balstad, T., Cauwelier, E., Cherbonnel, C., Consuegra, S., Coughlan, J., Cross, T.F., Crozier, W., Dillane, E., Ensing, D., de Leániz, C.G., García-Vázquez, E., Griffiths, A.M., Hindar, K., Hjorleifsdottir, S., Knox, D., Machado-Schiaffino, G., McGinnity, P., Meldrup, D., Nielsen, E.E., Olafsson, K., Primmer, C.R., Prodohl, P., Stradmeyer, L., Vähä, J.-P., Verspoor, E., Wennevik, V., Stevens, J.R.

Contemporary genetic structure of Atlantic salmon (Salmo salar L.) in the River Moy in Ireland is shown here to be strongly related to landscape features and population demographics, with populations being defined largely by their degree of physical isolation and their size. Samples of juvenile salmon were collected from the 17 major spawning areas on the river Moy and from one spawning area in each of five smaller nearby rivers. No temporal allele frequency differences were observed within locations for 12 microsatellite loci, whereas nearly all spatial samples differed significantly, suggesting that each was a separate population. Bayesian clustering and landscape genetic analyses suggest that these populations can be combined hierarchically into five genetically informative larger groupings. Lakes were found to be the single most important determinant of the observed population structure. Spawning area size was also an important factor. The salmon population of the closest nearby river resembled genetically the largest Moy population grouping. In addition, we showed that anthropogenic influences on spawning habitats, in this case arterial drainage, can affect relationships between populations. Our results show that Atlantic salmon biodiversity can be largely defined by geography, and thus, knowledge of landscape features (for example, as characterized within Geographical Information Systems) has the potential to predict population structure in other rivers without an intensive genetic survey, or at least to help direct sampling. This approach of combining genetics and geography, for sampling and in subsequent statistical analyses, has wider application to the investigation of population structure in other freshwater/anadromous fish species and possibly in marine fish and other organisms.

Cultured strains of marine and anadromous species reared for aquaculture can be either inadvertently (as in farm escapes) or deliberately (as in stocking/ ranching) introduced into the wild, where they may interact with wild conspecifics or other species. This chapter concentrates on the potentially detrimental genetic aspects of these interactions, largely in the context of species cultured in Europe but considering general principles, which have worldwide applicability. Most previous experimental work in the area has involved Atlantic salmon, which has the highest production of any finfish produced in Europe. These investigations have shown generally detrimental results for wild salmon populations, when interactions occur with reared strains. The various European species which might be affected by cultured introgressions (the major aquaculture species) are then considered under several headings: genetic composition of cultured strains compared with wild populations; modes of introduction into the wild; direct and indirect genetic interactions with wild populations/species; consequences of such interactions; establishing the severity of effects of wild/reared interactions with different spe- cies, utilising opportunist situations and field experiments; and, methods such as induction of sterility in reared strains to reduce detrimental effects. Relative risks for wild populations of the major aquaculture species are then considered, and general and specific genetic recommendations are presented.

In this study, the small subunit (18S) ribosomal DNA gene from an aurantiactinomyxon form of unknown taxonomic position (A1) and from its aquatic oligochaete host (Tubifex ignotus) were characterized. Molecular sequence information on A1 was obtained to allow comparisons of this gene with known sequences from known myxosporean forms, and therefore to investigate possible relationships between this organism and its alternate myxosporean stage. Sequence data for the oligochaete host, together with morphological features, will allow reliable identification of this species in the future. Sequence data derived from the 18S DNA gene and data from other related or non-related organisms were analyzed and used to construct a phylogenetic tree. Phylogenetic studies provided an insight into the taxonomic position of A1. Sequence similarities within the 18S rDNA A1 gene and compared organisms indicated that A1 was most closely related to members of the sub-order Variisporina (Myxidium lieberkuehni [Ml] and Sphaerospora oncorhynchi [So]). Clustering of the 3 organisms in the same branch was well supported by high bootstrap values (81%). A1 showed higher similarities with sequences of Ml (approximately 80%) than with So (approximately 79%). Myxosporean sequence analysis indicated that phylogenetic arrangements do not support traditional classification based on morphological criteria of the spores, but rather support arrangement by tissue location. Marine actinosporeans Triactinomyxon sp. and Tetraspora discoidea were found to be associated with Platysporinid myxosporeans, supporting previous findings. In this study, 18S rDNA sequence data are generated for first time for the aquatic oligochaete T. ignotus. Phylogenetic 18S rDNA gene analyses performed with T. ignotus support and confirm existing morphological and molecular phylogenetic studies. Paraphyly of the Tubificidae family was noticed.

Ostreid herpesvirus 1 (OsHV-1) and variants (OsHV-1 var, OsHV-1 µvar, Irish genotype) have had a significant impact on the Pacific oyster, Crassostrea gigas, industry worldwide and on the survival of larvae and juveniles of several other bivalve species in Europe. Diagnostic techniques used to screen for this pathogen include histology, polymerase chain reaction (PCR), and quantitative polymerase chain reaction (qPCR), which allows for quantification of the virus. Techniques used to confirm infection include PCR, in situ hybridization, and transmission electron microscopy, which have variable sensitivity and specificity. In this study, several new primers were designed to amplify the C region in the ORF4 gene of the virus. This region is variable and diagnostic among OsHV-1 and variants. To date, the routinely used C2/C6 primers, which are used to screen for OsHV-1 and variants, amplify a product of 709 bp whereas the new primers described in this study amplify products of 296 bp, 385 bp, and 400 bp. Several C. gigas samples, which had been exposed to herpes virus and variants were screened, and a sample of wild mussels (Mytilus spp.) was used as a negative control. The performance of the new PCR and primers was compared with the performance of the C2/C6 primers and qPCR. The effect of tissue storage and DNA extraction on PCR performance was also examined. The results of this study indicate that the new PCR and primers are more rapid, sensitive, and cost-effective compared with the C2/C6 PCR, and are as sensitive as qPCR. The results also highlight the impact that sample storage, tissue selection, DNA extraction method used, and subsequent storage of DNA have on PCR success or failure.

Conservation strategies for the critically endangered Bermuda skink will require knowledge of genetic variation and population structure. We describe the isolation of six polymorphic microsatellites for this species suitable for use in population genetics studies or for monitoring success of potential breeding programmes. Tissue sampling for DNA extraction involved no blood loss or tail autonomy. Three of these loci cross-amplify and are polymorphic in a related North American skink (Eumeces fasciatus) and should also be informative for this species.

Background Anadromous migratory fish species such as Atlantic salmon (Salmo salar) have significant economic, cultural and ecological importance, but present a complex case for management and conservation due to the range of their migration. Atlantic salmon exist in rivers across the North Atlantic, returning to their river of birth with a high degree of accuracy; however, despite continuing efforts and improvements in in-river conservation, they are in steep decline across their range. Salmon from rivers across Europe migrate along similar routes, where they have, historically, been subject to commercial netting. This mixed stock exploitation has the potential to devastate weak and declining populations where they are exploited indiscriminately. Despite various tagging and marking studies, the effect of marine exploitation and the marine element of the salmon lifecycle in general, remain the "black-box" of salmon management. In a number of Pacific salmonid species and in several regions within the range of the Atlantic salmon, genetic stock identification and mixed stock analysis have been used successfully to quantify exploitation rates and identify the natal origins of fish outside their home waters - to date this has not been attempted for Atlantic salmon in the south of their European range. Results To facilitate mixed stock analysis (MSA) of Atlantic salmon, we have produced a baseline of genetic data for salmon populations originating from the largest rivers from Spain to northern Scotland, a region in which declines have been particularly marked. Using 12 microsatellites, 3,730 individual fish from 57 river catchments have been genotyped. Detailed patterns of population genetic diversity of Atlantic salmon at a sub-continent-wide level have been evaluated, demonstrating the existence of regional genetic signatures. Critically, these appear to be independent of more commonly recognised terrestrial biogeographical and political boundaries, allowing reporting regions to be defined. The implications of these results on the accuracy of MSA are evaluated and indicate that the success of MSA is not uniform across the range studied; our findings indicate large differences in the relative accuracy of stock composition estimates and MSA apportioning across the geographical range of the study, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the area studied. This result probably reflects the more genetically distinct nature of populations in the database from Spain, northwest France and southern England. Genetic stock identification has been undertaken and validation of the baseline microsatellite dataset with rod-and-line and estuary net fisheries of known origin has produced realistic estimates of stock composition at a regional scale. Conclusions This southern European database and supporting phylogeographic and mixed-stock analyses of net samples provide a unique tool for Atlantic salmon research and management, in both their natal rivers and the marine environment. However, the success of MSA is not uniform across the area studied, with large differences in the relative accuracy of stock composition estimates and MSA apportioning, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the region. More broadly, this study provides a basis for long-term salmon management across the region and confirms the value of this genetic approach for fisheries management of anadromous species.